Strain identifier

BacDive ID: 453

Type strain: Yes

Species: Paraglaciecola polaris

Strain history: CIP <- 2004, S. Van Trappen, Ghent Univ., Ghent, Belgium <- T.L. Tan, Wegener Inst.: strain ARK 150

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General

@ref: 6448

BacDive-ID: 453

DSM-Number: 16457

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, motile, rod-shaped

description: Paraglaciecola polaris DSM 16457 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from sea water .

NCBI tax id

NCBI tax idMatching level
1129793strain
222814species

strain history

@refhistory
6448<- S. Van Trappen; ARK 150 <- T. L. Tan
121925CIP <- 2004, S. Van Trappen, Ghent Univ., Ghent, Belgium <- T.L. Tan, Wegener Inst.: strain ARK 150

doi: 10.13145/bacdive453.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Paraglaciecola
  • species: Paraglaciecola polaris
  • full scientific name: Paraglaciecola polaris (Van Trappen et al. 2004) Shivaji and Reddy 2014
  • synonyms

    • @ref: 20215
    • synonym: Glaciecola polaris

@ref: 6448

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Paraglaciecola

species: Paraglaciecola polaris

full scientific name: Paraglaciecola polaris (Van Trappen et al. 2004) Shivaji and Reddy 2014

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31245negative2.5 µm0.4 µmrod-shapedyes
69480yes98.57
69480negative99.998
121925negativerod-shapedyes

pigmentation

  • @ref: 31245
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6448BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
36580Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121925CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6448positivegrowth20psychrophilic
31245positivegrowth05-30
31245positiveoptimum17.5psychrophilic
36580positivegrowth20psychrophilic
121925positivegrowth5-25psychrophilic
121925nogrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 31245
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.966

halophily

@refsaltgrowthtested relationconcentration
31245NaClpositivegrowth<10 %
31245NaClpositiveoptimum5 %
121925NaClpositivegrowth2-6 %
121925NaClnogrowth0 %
121925NaClnogrowth8 %
121925NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3124530089acetate+carbon source
3124516449alanine+carbon source
3124518403L-arabitol+carbon source
3124517057cellobiose+carbon source
3124523652dextrin+carbon source
3124528757fructose+carbon source
3124528260galactose+carbon source
3124517234glucose+carbon source
3124529987glutamate+carbon source
3124528087glycogen+carbon source
3124517716lactose+carbon source
3124525017leucine+carbon source
3124517306maltose+carbon source
3124529864mannitol+carbon source
3124537684mannose+carbon source
3124528053melibiose+carbon source
3124537657methyl D-glucoside+carbon source
3124551850methyl pyruvate+carbon source
3124517272propionate+carbon source
3124516634raffinose+carbon source
3124517814salicin+carbon source
3124517992sucrose+carbon source
3124527082trehalose+carbon source
3124553423tween 40+carbon source
3124553426tween 80+carbon source
312454853esculin+hydrolysis
1219254853esculin-hydrolysis
12192517632nitrate-reduction
12192516301nitrite-reduction
121925132112sodium thiosulfate-builds gas from

metabolite production

  • @ref: 121925
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31245acid phosphatase+3.1.3.2
31245alkaline phosphatase+3.1.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121925oxidase+
121925beta-galactosidase+3.2.1.23
121925alcohol dehydrogenase-1.1.1.1
121925gelatinase+/-
121925amylase+
121925caseinase+3.4.21.50
121925catalase+1.11.1.6
121925tween esterase+
121925lecithinase+
121925lipase+
121925lysine decarboxylase-4.1.1.18
121925ornithine decarboxylase-4.1.1.17
121925protease+
121925tryptophan deaminase-
121925urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121925+++++++---+++---+---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121925+-++---+-+-++--++++--+-----------+------------------------------------------------------+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryisolation date
6448sea water (25m depth)Arctic Ocean
121925Environment, Arctic sea waterWestern Greenland Sea1997

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_6761.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_98;96_345;97_456;98_525;99_6761&stattab=map
  • Last taxonomy: Paraglaciecola polaris
  • 16S sequence: AJ293820
  • Sequence Identity:
  • Total samples: 560
  • soil counts: 1
  • aquatic counts: 515
  • animal counts: 41
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64481Risk group (German classification)
1219251Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6448
  • description: Glaciecola polaris 16S rRNA gene, type strain LMG 21857
  • accession: AJ293820
  • length: 1485
  • database: ena
  • NCBI tax ID: 222814

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraglaciecola polaris LMG 21857GCA_000315055contigncbi1129793
66792Glaciecola polaris LMG 218571129793.3wgspatric1129793
66792Paraglaciecola polaris LMG 218572531839185draftimg1129793

GC content

  • @ref: 31245
  • GC-content: 44.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.678yes
flagellatedyes83.662no
gram-positiveno99.065yes
anaerobicno98.418yes
halophileyes64.193yes
spore-formingno97.369no
glucose-utilyes93.676yes
aerobicyes87.863yes
glucose-fermentno79.274no
thermophileno99.696yes

External links

@ref: 6448

culture collection no.: DSM 16457, CIP 108324, LMG 21857, ARK 150

straininfo link

  • @ref: 70132
  • straininfo: 28694

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15388742Glaciecola polaris sp. nov., a novel budding and prosthecate bacterium from the Arctic Ocean, and emended description of the genus Glaciecola.Van Trappen S, Tan TL, Yang J, Mergaert J, Swings JInt J Syst Evol Microbiol10.1099/ijs.0.63123-02004Alteromonadaceae/*classification/cytology/*isolation & purification/physiology, Antarctic Regions, Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Genes, rRNA, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Water MicrobiologyEnzymology
Phylogeny17473239Glaciecola agarilytica sp. nov., an agar-digesting marine bacterium from the East Sea, Korea.Yong JJ, Park SJ, Kim HJ, Rhee SKInt J Syst Evol Microbiol10.1099/ijs.0.64723-02007Agar/metabolism, Alteromonadaceae/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, Carbon/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA/genetics, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, TemperatureMetabolism
Metabolism28044272Gene cloning and expression of a glucoside 3-dehydrogenase from Sphingobacterium faecium ZJF-D6, and used it to produce N-p-nitrophenyl-3-ketovalidamine.Zhang JF, Chen WQ, Chen HWorld J Microbiol Biotechnol10.1007/s11274-016-2187-02017Bacterial Proteins/genetics/metabolism, Cloning, Molecular/*methods, Escherichia coli/genetics/metabolism, Galactosides/metabolism, Glucose Dehydrogenases/*genetics/*metabolism, Glucosides/metabolism, Hydrogen-Ion Concentration, Nitrophenols/*metabolism, Recombinant Proteins/metabolism, Sequence Homology, Amino Acid, Sphingobacterium/*enzymology/genetics, Substrate Specificity, TemperatureEnzymology
Phylogeny32687464Paraglaciecola marina sp. nov., isolated from marine alga (Sargassum natans (L.) Gaillon).Wang Y, Zhang Y, Liu T, Zhu X, Ma J, Su X, Kang J, Guo CInt J Syst Evol Microbiol10.1099/ijsem.0.0041322020Alteromonadaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sargassum/*microbiology, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6448Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16457)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16457
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31245Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2756828776041
36580Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5934
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
70132Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID28694.1StrainInfo: A central database for resolving microbial strain identifiers
121925Curators of the CIPCollection of Institut Pasteur (CIP 108324)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108324